Title: Make Forest Plot with GWAS Data
Version: 1.0.0
Description: Extract and reform data from GWAS (genome-wide association study) results, and then make a single integrated forest plot containing multiple windows of which each shows the result of individual SNPs (or other items of interest).
URL: https://github.com/yilixu/gwasforest
BugReports: https://github.com/yilixu/gwasforest/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: colorspace, data.table, dplyr, ggplot2, ggrepel, glue, utils
NeedsCompilation: no
Packaged: 2020-11-22 11:06:46 UTC; yilixu
Author: Yili Xu [aut, cre], Anqi Wang [aut]
Maintainer: Yili Xu <yilixu@usc.edu>
Repository: CRAN
Date/Publication: 2020-11-24 08:30:03 UTC

Make forest plot with GWAS data

Description

Extract and reform data from GWAS results, and then make a single integrated forest plot containing multiple windows of which each shows the result of individual SNPs (or other items of interest).

Usage

gwasforest(
  customFilename,
  customFilename_results = NULL,
  customFilename_studyName = NULL,
  keepStudyOrder = TRUE,
  stdColnames = FALSE,
  customColnames = NULL,
  calculateEXP = FALSE,
  calculateCI = TRUE,
  valueFormat = "Effect",
  metaStudy = "Study1",
  colorMode = "mono",
  forestLayout = "auto",
  plotTitle = "auto",
  showMetaValue = TRUE,
  outputFolderPath = NULL
)

Arguments

customFilename, customFilename_results

string, relative or full path to the input file. customFilename for raw GWAS data file, and customFilename_results for gwasforest-generated results file. If customFilename_results is provided, certain downstream calculations will be skipped.

customFilename_studyName

(optional) string, relative or full path to the study name file, required if users want to use their own study names which is not standardized (see "stdColnames"); all study names should be in one column with a header; also, study names should be in the order of that they first appear in the input data columns.

keepStudyOrder

logical, whether to keep studies (except for meta study) in the original order provided by user (from customFilename_studyName), or sort them alphabetically on the combined forest plot; meta study will always be put at the bottom of the combined forest plot.

stdColnames

logical, whether the input data has standardized column names as provided in the instruction example, if TRUE, column order doesn't matter (except that study1 needs to be the Meta study); if FALSE, see "customColnames".

customColnames

character, case-sensitive, can be a vector, choose from c("Value", "StdErr") or c("Value", "Upper", "Lower") based on what columns are contained in the input data; required if stdColnames = FALSE, also the input data need to be grouped by study while in the customColnames order, e.g. Study1__Value, Study1__StdErr, Study2__Value, Study2__StdErr...; in addition, each study should contain the same number of columns.

calculateEXP

logical, whether to calculate exp(Value), if TRUE, downstream calculateCI will also take exp into consideration.

calculateCI

logical, whether to calculate Confidence Interval, if TRUE, input data need to contain "StdErr" column; if FALSE, input data need to contain "Upper" and "Lower" columns.

valueFormat

character, format of Value column, e.g. "Effect", "Beta", "OR", "HR", "logRR"...

metaStudy

character, which study is the meta study, by default "Study1" (the first study appear in the input data columns).

colorMode

character, choose from c("mono", "duo", "diverse"), mono - render all studies including meta study in the same color, duo - highlight meta study, diverse - render all studies in different colors.

forestLayout

character, or integer vector, determines the layout of the combined forest plot, by default use "auto" which will automatically arrange the combined forest plot; or user can explicitly set the row/column layout by providing a vector c(rowNum, colNum).

plotTitle

character/string, the title of the combined forest plot, can be customized or simply set to "auto".

showMetaValue

logical, whether to show value for meta group on the combined forest plot.

outputFolderPath

string, relative or full path to the output folder, can be set to NULL (no output file will be written to the file system).

Value

list, users can run the function without assigning the return value to a variable. If assigned to a variable, it will be a list containing GWAS results (dataframe) and GWAS forest plot (ggplot2 object).

Examples

# customFilename in dataframe format (with standardized column names)
tempValue = runif(n = 18, min = 0.01, max = 2)
tempStdErr = tempValue / rep(3:5, times = 6)
eg_customFilename = data.frame(paste0("Marker", 1:6), tempValue[1:6],
    tempStdErr[1:6], tempValue[7:12], tempStdErr[7:12], tempValue[13:18],
    tempStdErr[13:18], stringsAsFactors = FALSE)
colnames(eg_customFilename) = c("MarkerName", paste0(rep("Study", times = 6),
    rep(1:3, each = 2), sample(LETTERS, 6)))
rm(tempValue, tempStdErr)
eg_customFilename_studyName = data.frame("studyName" = paste0("Study", 1:3),
    stringsAsFactors = FALSE)
eg_returnList = gwasforest(eg_customFilename, customFilename_studyName =
    eg_customFilename_studyName, stdColnames = FALSE, customColnames = c("Value",
    "StdErr"), valueFormat = "Effect", metaStudy = "Study1", colorMode = "duo")

# customFilename in dataframe format (without standardized column names),
# with customFilename_studyName provided in dataframe format
tempValue = runif(n = 18, min = 0.01, max = 2)
tempStdErr = tempValue / rep(3:5, times = 6)
eg_customFilename = data.frame(paste0("Marker", 1:6), tempValue[1:6],
    tempStdErr[1:6], tempValue[7:12], tempStdErr[7:12], tempValue[13:18],
    tempStdErr[13:18], stringsAsFactors = FALSE)
colnames(eg_customFilename) = c("MarkerName", paste0(rep("Study", times = 6),
    rep(1:3, each = 2), sample(LETTERS, 6)))
rm(tempValue, tempStdErr)
eg_customFilename_studyName = data.frame("studyName" = paste0("Study", 1:3),
    stringsAsFactors = FALSE)
eg_returnList = gwasforest(eg_customFilename, customFilename_studyName =
    eg_customFilename_studyName, stdColnames = FALSE, customColnames = c("Value",
    "StdErr"), valueFormat = "Effect", metaStudy = "Study1", colorMode = "duo")

# customFilename_results in dataframe format (run either of the two examples
# above to see the example results)
eg_customFilename_results = eg_returnList[[1]]